Source code for tvb.adapters.uploaders.gifti_surface_importer

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.. moduleauthor:: Mihai Andrei <>
.. moduleauthor:: Calin Pavel <>

from tvb.adapters.uploaders.gifti.parser import GIFTIParser
from tvb.basic.logger.builder import get_logger
from tvb.basic.neotraits.api import Attr, EnumAttr
from tvb.core.adapters.exceptions import LaunchException, ParseException
from tvb.core.adapters.abcuploader import ABCUploader, ABCUploaderForm
from tvb.adapters.datatypes.db.surface import SurfaceIndex
from tvb.core.neotraits.forms import SelectField, TraitUploadField, BoolField
from tvb.core.neotraits.uploader_view_model import UploaderViewModel
from tvb.core.neotraits.view_model import Str
from tvb.datatypes.surfaces import SurfaceTypesEnum

[docs]class GIFTISurfaceImporterModel(UploaderViewModel): file_type = EnumAttr( label='Specify file type : ', default=SurfaceTypesEnum.CORTICAL_SURFACE ) data_file = Str( label='Please select a .gii (LH if cortex)' ) data_file_part2 = Str( required=False, label="Optionally select 2'nd .gii (RH if cortex)" ) should_center = Attr( field_type=bool, required=False, default=False, label='Center surface using vertex means along axes' )
[docs]class GIFTISurfaceImporterForm(ABCUploaderForm): def __init__(self): super(GIFTISurfaceImporterForm, self).__init__() self.file_type = SelectField(GIFTISurfaceImporterModel.file_type, name='file_type') self.data_file = TraitUploadField(GIFTISurfaceImporterModel.data_file, '.gii', 'data_file') self.data_file_part2 = TraitUploadField(GIFTISurfaceImporterModel.data_file_part2, '.gii', 'data_file_part2') self.should_center = BoolField(GIFTISurfaceImporterModel.should_center, name='should_center')
[docs] @staticmethod def get_view_model(): return GIFTISurfaceImporterModel
[docs] @staticmethod def get_upload_information(): return { 'data_file': '.gii', 'data_file_part2': '.gii' }
[docs]class GIFTISurfaceImporter(ABCUploader): """ This importer is responsible for import of surface from GIFTI format (XML file) and store them in TVB as Surface. """ _ui_name = "Surface GIFTI" _ui_subsection = "gifti_surface_importer" _ui_description = "Import a surface from GIFTI"
[docs] def get_form_class(self): return GIFTISurfaceImporterForm
[docs] def get_output(self): return [SurfaceIndex]
[docs] def launch(self, view_model): # type: (GIFTISurfaceImporterModel) -> [SurfaceIndex] """ Execute import operations: """ parser = GIFTIParser(self.operation_id) try: surface = parser.parse(view_model.data_file, view_model.data_file_part2, view_model.file_type, should_center=view_model.should_center) surface.compute_triangle_normals() surface.compute_vertex_normals() validation_result = surface.validate() if validation_result.warnings: self.add_operation_additional_info(validation_result.summary()) surface_idx = self.store_complete(surface) return [surface_idx] except ParseException as excep: logger = get_logger(__name__) logger.exception(excep) raise LaunchException(excep)